DESCRIPTION

AMoRe includes routines to run a complete molecular replacement.

As well as carrying out ROTATION and TRANSLATION searches against various targets, and doing RIGID BODY REFINEMENT,
there are routines to reformat the observed data from the new crystal form, and
to generate and tabulate structure factors from the model in a large P1 cell. See reference [1].

The steps are usually carried out in the following order:

The observed data is extended to cover a hemisphere of reciprocal space
and reformatted.

Structure factors for the model are tabulated on a fine grid (corresponding
to a large "unit cell"). This is the key to the program's speed. All subsequent
structure factors required for the searches are obtained by interpolating into
this table. The structure factors can be calculated within AMoRe from a set of
coordinates, using the option TABFUN, or generated outside the program and read
in using the option SORTFUN.

The rotation function is run searching for Patterson correlation within
a sphere centred on the origin. This allows the Patterson to be expressed in terms
of spherical harmonics, and the calculation to exploit FFT techniques. Two different
types of indicators of a good solution are given (see also below):

The correlation between the observed and model pattersons;

Correlation coefficients and Rfactors between the observed Fs or Is and
generated Fs or Is from a model with the given orientation.

AMoRe requires a LOT of memory and this may cause problems on some machines.
However this new release is considerably less demanding than the older one
(see Memory allocation).

Table of the finely sampled inverse Fourier coefficients (i.e., structure
factors which have been read in from a previously prepared MTZ file). These
must extend a little past the required resolution of the calculations
to allow for interpolation.
This is a binary file which also holds the large "unit cell",
maximum h, k, l, and resolution (see example [2]).

Option 1:

Packs and sorts H K L [Fobs SigFobs] or [W*Fobs PhiObs] to an internal form for use
in later steps.

Option 2:

Packs an input list of H K L FC PHIC for use as a table. This format is described
below. This gives the user great flexibility to try different
types of search models. For example, structure factors can be generated from
modified electron density maps, or calculated structure factors can be
converted to E values (see example [2]).

The model coordinates are translated so that their centre of gravity is at the
origin. They can then be rotated so that the principal axes of inertia
of the model are parallel to the a, b and c axes of the "minimal box" which
just contains the model. The dimensions of the "minimal box" are determined,
and the "maximum distance" of any coordinate from the centre of mass.
You may choose not to ROTATE the model; in some cases results may then be simpler
to interpret. For instance if you want to compare results from several models it is
convenient to allow
the first model to ROTATE, then to fit all others to these repositioned coordinates
which will have been output to the assigned XYZOUT. It may also be useful if you expect some predictable
result; e.g. that the new crystallographic symmetry axes should map onto those of the model structure.
Hint: It can help to understand results if some "pseudo" atoms are added
to the model PDB file. For example if you have a two fold axis in the
original structure put 2 coordinates on this axis. If the model forms a
tetramer centred at (Xt,Yt,Zt) include this coordinate plus 3 which lie
on the tetramer axes.

Structure factors are generated from the modified coordinates for a
"CELL" with dimensions SCALE*minimal_a, SCALE*minimal_b,
SCALE*minimal_c and all angles = 90 . SCALE has the default value of 4, but
can be reset by the SAMPLE keyword. All later
structure factors and gradients for the model in its various orientations
are interpolated from this data.

Step_3c ROTATION_Stage

For the CROSS rotation function the output rotational solutions
are given in terms of the Eulerian angles,
alpha, beta and gamma with each line flagged: SOLUTIONRC.

The Eulerian angles use the convention described by Tony Crowther which
is used in all CCP4 programs, e.g. ALMN, LSQKAB,
PDBSET and DM. They define a rotation matrix which moves
the model molecule into the proper orientation for the new crystal form.
The model is first rotated through gamma about Zo, then through beta about the new Yo,
then through alpha about the new Zo.
Positive rotation is clockwise when looking along the axis from the origin.
See elsewhere for details of the definitions of the rotation matrix and the
orthogonalisation conventions which define Zo Yo and Xo.

Four solution criteria are tabulated:

CC_F is the correlation coefficient between the observed amplitudes
for the crystal and the calculated amplitudes for the model. It is surprising
that this is a satisfactory target, since the model amplitudes are generated
in a P1 cell, but it does seem to be the most effective discriminator. It is sensible
to sort the solutions on this target.

RF_F is the classic R factor between the observed amplitudes
for the crystal and the calculated amplitudes for the model. Again, it is
surprising that this is a satisfactory target, since the model amplitudes
are generated in a P1 cell, but it does seem to be reasonable, although
the CC_F is probably better.

CC_I is the correlation coefficient between the observed intensities
for the crystal and the sum of calculated intensities for all symmetry
equivalents of the model, i.e. the intensities are summed, but without
any correction for the relative positioning of the symmetry related
molecules.

CC_P is the Patterson correlation coefficient between the crystal and
the model pattersons evaluated within the defined sphere centred on the
Patterson origin.

or SOLUTIONRS

For the SELF rotation function the solution is given in terms of Eulerian and
polar angles with each line flagged: SOLUTIONRS.

If Kappa is 180 or 120 then you may have a 2-fold or a 3 fold rotation between
NCS related molecules.

(defaults estimated from crystal cell, and the dimensions of the model table). These can be reset if necessary.)

Input:

A list of solutions to the Rotation function output obtained in Step_3.

The search for several molecules can be done by finding first one molecule,
then FIXing it whilst searching for a second molecule, etc.

Output:

A list of solutions flagged as: SOLUTIONTF.

Each has:
Alpha_i Beta_i Gamma_i Xf_i Yf_i Zf_i CC_F RF_F CC_I Dmin.

The Xf, Yf and Zf are fractions of the observed unit cell edges.
CC_F RF_F CC_I are described above.
Dmin is the shortest distance between the centres of mass
of the symmetry equivalent molecules. This can be used to identify solutions
which overlap their symmetry mates.

Output:

MAPOUT

A map of the translation function can be output in the standard CCP4 format.

This is assigned to MAPOUT and can be contoured in the usual way (NPO).
The same file assignment is used for each TRANSLATION search
you make, so if you want to contour your favourite solution you will need
to rerun the calculation with only that SOLUTION. Remember it may be very
large; assign it to a scratch area, or /dev/null if this causes problems.

Step_5 FITFUN

Performs rigid-body refinement for any specified solution of the rotation
or translation search, see reference [5].

Input:

HKLPCK0

Crystal h k l output by SORTING step.

Input:

table<i>

For any model(s) you wish to use.

Optional Input:

Memory allocation parameters

FITING_MEQ, FITING_MT, FITING_NR, FITING_NP

(defaults estimated from crystal cell, and the dimensions of the model table). These can be reset if necessary.)

Input:

A list of solutions.

Output:

A list of solutions flagged as: SOLUTIONF.

They are given as: Alpha_i Beta_i Gamma_i Xf_i Yf_i
Zf_i CC_F RF_F CC_I with the conventions described above.

Check that the CCs and RF_F have improved.

Step_6 REORIENTATE

This works out the appropriate rotation and translation parameters to
apply to the initial model (can also be done while running ROTFUN or FITFUN).

Input:

Centre of Mass and Eulerian angles which were applied to the original MODEL in TABFUN.

Input:

The refined rotation and translation parameters output by FITFUN.

Input:

HKLPCK0

To extract the unit cell of new crystal form.

Output:

A list of solutions given as:

Alpha_i Beta_i Gamma_i XA_i YA_i
ZA_i Correlation_coefficient_i Rfactor_i. The XA, YA and ZA are given in
Angstroms. Each line is flagged: Shifted_sol.

LIKELY PROBLEMS

Some common errors:

You must run both CLMN calculations with the same resolution limits
and sphere radius.

The HKLPCK files all pack the hkl and symmetry flag into one integer. The
program checks the maximum values of H K L and NM ( = 2*Nsym_primitive + 1) allowed
for packing into a 32 bit integer. This is most restrictive at the Translation
function stage which needs to store coefficients for all reflection pairs;
H-Hj, K-Kj L-Lj where the Hj, Kj, and Lj are symmetry equivalents of H,K,& L,
thus needs maximum values for the coefficients which are double the actual ones
for the data.

KEYWORDED INPUT

The various data control lines are identified by keywords. Only the
first 4 characters of a keyword are significant. Records may be continued
across line breaks using & or - as the last character on the line to
be continued. The available keywords are listed below grouped according
to their function:

General Keywords used at any stage:

VERBOSE

produces lots of output.

TITLE

to help you know what you did.

Function keywords:

These call the appropriate procedures.

SORTFUN

calls SORTING procedure to sort and pack reflections.

TABFUN

calls TABLING procedure to prepare structure factors from the model.

ROTFUN

calls ROTING procedure for the rotation function (must be followed
by GENE and/or CLMN and/or ROTA).

TRAFUN

calls TRAING procedure for the translation function.

FITFUN

calls FITING procedure for rigid body fitting.

SHIFT

calls REORIENTATE procedure to apply shifts to the model final solution.

SORTFUN keywords

SORTFUN [ RESOLUTION <rmin> <rmax> ] [ MODEL ]

This signals the beginning of Step_1 SORTFUN.

RESOLUTION

<rmin> and <rmax> define the resolution range for all
statistics. Can be put in as 4sin(theta)**2/lambda**2 limits, or as Angstrom
limits in any order (defaults to MTZ resolution). Data output to HKLPCK0
are restricted to the outer resolution cutoff.

MODEL

This signals that the structure factors input from HKLIN are to be
used to make a table. This requires that they have been calculated from
a model placed in a large unit cell and therefore the structure factors are sampled on a very fine grid.
(See part of example [2]).

LABIN <column_assignment> ...

[Compulsory]

A line giving the names of the input data items to be
selected followed by <program_label>=<file_label> assignments.
Acceptable labels are:

FP SIGFP PHI [W] FC PHIC

FC PHIC must be assigned for structure factors input.
FP must be assigned for creating the list of observations.
If PHI and optionally W is assigned, W*FP and PHI are stored and can be used for phased translation searches.

TABFUN keywords

TABFUN [ NOROTATE ] [ NOTRANSLATE ] [ NOTAB ] [ HKLOUT ] [ SFOUT ]

This signals the beginning of Step_2 TABFUN.

NOROTATE

Do not rotate the model before initialising calculation.

NOTRANSLATE

Do not translate the model before initialising calculation.

Use this extremely rarely. AMoRe assumes your molecule lies roughly at the
origin of the test cell. If you have already run TABFUN, and you wanted
to carve pieces out of XYZOUT to do rigid body fitting on segments, it
is useful to make a table for each fragment with the TABFUN NOROTATE NOSHIFT option.
Similarly if you want to fit another possible model over the first XYZOUT.
NEVER use this in an initial pass.

NOTAB

Does not produce a table - just orientate the molecule if appropriate
and move the molecule's centre of mass to the origin. This coordinate file
can then be used to calculate structure factors and generate Es which can
be read in to produce a table file.

HKLOUT

The contents of the table can also be output as an ASCII list of H K L FC PHIC. This may
be useful for checking.

SAMPLE <i> [ RESOLUTION <dmin> SCALE <scale> SHANNON <sharat> ]

<i> is the model number and is followed by the sampling control parameters.

RESOLUTION <dmin>

<dmin> (in Angstroms) is the resolution limit of generated structure
factors. There is no point in setting this higher than the maximum resolution
given in SORTFUN.

SCALE <scale>

Optional: default = 4.

A model `cell' created equal to (minimal box)*<scale>. This
controls how finely the model structure factors are sampled in reciprocal space.

SHANNON <sharat>

<sharat> is the Shannon rate for sampling the coordinate map.
The default is 2.5. If the B factors have been sharpened it is wise to use
a finer grid, i.e. increase <sharat> to 3.5 or 4.

Example:

SAMPLE 1 RESO 3 SHANN 2.5 SCALE 4.0

ROTFUN Keywords {Step_3}

ROTFUN

This signals the beginning of Step_3 ROTFUN with subsequent keywords as follows.

Generate {Step_3a}

GENERATE <i> [ RESOLUTION <rmin> <rmax> CELL_MODEL <a> <b> <c> ]

<i> is the model number.
This routine calculates the model `structure factors' in a suitable P1
cell, and writes them in the same format as the SORTFUN output for the
crystal amplitudes. The file is assigned to HKLPCK1.

RESOLUTION <rmin> <rmax>

Resolution range for data output. Can be put in as 4sin(theta)**2/lambda**2
or as Angstrom limits in either order. Choose the maximum resolution you
may wish to use; this step need only be run once for each model and a subset
extracted with the resolution limits given in CLMN.

Orthogonalisation code (see below for code). Only needed for CRYSTAL.
Except for monoclinic spacegroups with B unique, when ORTH = 3 may be useful,
all orthogonalisation codes
should be set to 1. Even for the monoclinic case it is usually easier to
leave the code as 1.

(default ORTH=1)

FLIM <fmin> <fmax>

Minimum and maximum values of F used (rarely used option).

SHARP or BADD<badd>

Sharpening B value for structure factors. This can be used to modify
the input F by exp**{-<badd>*sin**2(theta)/lambda**2} before squaring,
i.e. a negative <badd> will sharpen the data.

RESOLUTION <rmin> <rmax>

Can be put in as 4sin(theta)**2/lambda**2 or as Angstrom limits in
either order. These limits will truncate the H K L listed in HKLPCK. It
is important that the SAME resolution limits are used for both the MODEL
and the CRYSTAL.

SPHERE <Irmax>

<Irmax> is the radius of the integration sphere in Angstroms.
Tips:

This should not be greater than your model's Maximal distance from
Centre of Mass output by TABFUN. David Blow points out that for a spherical
molecule 75-80% of the molecular diameter includes about 80% of the integrated
Patterson density. Ian Tickle suggests using 75% of the minimum diameter
in general.

The volume of the sphere should probably not exceed the volume of the
asymmetric unit.

If the radius is greater than half the minimum cell edge you will be
including some Patterson vectors twice. Opinions differ on how important
this is, but the program warns about this case.

Other factors like the shape of the model may influence you; remember
this is the RADIUS within which the interesting self vectors should lie.

Flags whether calculation is to be a SELF rotation, which will only
need CLMN0 as input, or a CROSS rotation function which will need CLMN0
and some CLMN<i>. The correlation between self- and cross-rotation
functions can be analysed with the program RFCORR.

MODEL <i>

HKLPCK<i> for MODEL <i>.

BESLIM <lmin> <lsup>

Expansion using spherical harmonic functions between <lmin>
and <lsup> is done. Low order terms (i.e. for l = 2 or 4) tend to
be governed by the crystal symmetry; excluding them may reduce the final
peak heights, but make the rotation parameters more precise and make multiple
solutions have more equal heights. The upper cut off is governed by the
ratio of the integration radius to the resolution. The upper default is 500.
The lower cut off has a similar effect to the inner cutoff radius for the
Patterson vectors. However in some cases it helps to include all terms. Now
the default is to test all lower limits of 2, 4, 6, 8 and 10 and see which gives the
best contrast.

The angles MUST refer to the SAME orthogonalisation convention as you are using for the CROSS
rotation. See example [3].

If there are several molecules in the crystal asymmetric unit, AND you know the rotations
which relate them to each other, i.e you have a solutions to the SELF ROTATION,
then the solutions to the cross rotation can be searched to find sets which are related by the expected
NCS operators. If you do not have a closed group things are messy. The self rotation always finds
pairs of solutions, i.e. that which rotates Mol1 to Mol2, and that which rotates Mol2 to Mol1.
These are the inverse of each other; in Polar coordinates, they have the form (Omega,Phi,Kappa)
and (Omega,Phi,-Kappa), and the Eulerian equivalent is (Alpha, Beta, Gamma) and (-Gamma,-Beta, -Alpha).

It is not altogether easy to decide what to do, and you need to have some idea of how many
molecules you expect to find in the asymmetric unit, and how they may be arranged.
This can be complicated to sort out; if there is a hexamer in the crystal,
you would expect to find 3 two-fold axes, all perpendicular to a three fold axis -
if two axes are perpendicular, look at the product of their direct cosines:

For TRAP, where the 11-fold rotation axis is perpendicular to a crystallographic
2 fold axis, the self rotation showed both a single peak at (Omega, Phi, 360/11) and
11 2-fold axes. This did NOT mean that TRAP contained 11 dimers, although the self
rotation results were consistent with such a conclusion.
AMoRe does not at present generate all symmetry equivalents of SELF rotation solutions
so it is sensible to use ROTMAT to give a complete list.

If you believe you have a proper rotation with a clear solution with Kappa equal 360/n,
Kappa =180 ( 2-fold), or 120 (3-fold) or 72 (5-fold) and the NCS operators form closed group,
then you would specify NROT = n-1, followed by n-1 sets of polar angles to define the rotations:
(Omega,Phi,360/n) and (Omega,Phi,2*360/n) etc. In this case, every self rotation solution
and its inverse belong to the set.

If say, you expect 222 NCS symmetry with 3 intersecting 2-fold axes, you would set
NROT="3" and specify the three sets of
two fold axes: (Omega1,Phi1,180), (Omega2,Phi2,180) and (Omega3,Phi3,180).

Reorientation {Step_3d}

Reorientate stage. Moves Eulerian angle solutions determined for shifted
model stored in XYZOUT<Model_number> to give solutions to be applied
to original model. Needed if you want your solutions converted back to
ones to apply to original coordinates.

COM <Xcom> <Ycom> <Zcom>

Coordinates of the molecule's centre of mass output by TABFUN.

EULER <alpha> <beta> <gamma>

Rotation angles applied to the original model output by TABFUN.

Example

SHIFT 1 COM 17.3 -10.5 28.7 EULER 301.2 35.7 185.2

TRAFUN keywords {Step_4}

There are various translation function targets. Each takes each orientation
solution in turn and searches for the NPIC "best" translational Xi Yi Zi for this orientation.
Good solutions should give high correlation coefficients
between FP and FC, and low Rfactors. Only one target can be specified for each run.

CB | CO - the method of Crowther and Blow (default).

CB(T) = <DeltaI(obs) * I(calc)(T)>

The convolution (designated by "*") of the observed
Patterson (after subtraction of the contribution of the self vectors)
with the calculated one for each value of the translation vector T.

PT | PTF - Phased translation function.

This can either use externally generated phases for the model (option PTF; input at SORTFUN)
or for many body problems phases derived from the FIXed molecules (option PT).

It looks for the best overlap of the 2 maps: (Fp:PHI model) and (Fc:PHI model).
See reference [4].

Each function tests each orientation solution in turn and searches for the best
translational Xi Yi Zi for this orientation. Good solutions should give
high correlation coefficients between FP and FC, and low Rfactors.
For the first molecule all <Xi> <Yi> <Zi> belonging
to the Cheshire cell are searched (see reference [7]). The Cheshire cell is
the minimum volume which will allow a unique solution. For the first molecule
it will be the cell which covers a volume from one possible origin to the
next - you can usually see it by inspection of International Tables, e.g.:
For P212121, the Cheshire cell is 0-0.5,0-0.5,0-0.5. For P21 the Cheshire
cell is 0-0.5,any y,0-0.5. If you are searching for the NMOLth molecule
of a set, the Cheshire cell will now be the whole primitive volume. You
have assigned the origin by choosing the position of the first molecule,
and the other molecules will have to be positioned relative to that choice.

A map of the Cheshire cell for each search is written to the file assigned
to MAPOUT. N.B. the same file is used for all solutions - only the final
one will be saved. If you wish to plot your best solution you will have
to recalculate it.

Translation functions use a great deal of memory.
The whole FFT transform is held in memory at once, and the calculation
is done over a set of reciprocal lattice coefficients which can be twice
the size of Hmax, Kmax, Lmax.

NMOL <nmol>

Number of molecules to search for (maximum 65). The program assumes
you have solutions for <nmol>-1 molecules and searches for the best
fit for the <nmol>-th one. The <nmol>-1 solutions must be FIXed;
see examples [1f], [1g], [1h]. Default = 1.
It is more complicated if you are using a NCS translation vector.

NCSTRANS <U_vec> <V_vec> <W_vec>

If there is a non-crystallographic translation between two molecules
in the unit cell, this will be indicated by a large ( > 20% of origin) peak in the native
4Å Patterson; see CCP4i Task: Analyse Data for MR) it is best to search for the two
related molecules at the same time. You need to give the TRAFUN the coordinates of the Patterson vector,
<U_vec> <V_vec> <W_vec>. This always requires that <nmol>
is advanced by 2 for the next cycle of TRANSLATION searching.
For the first pass, set nmol as 1, and the program will position a pair of molecules
with the same orientation, and translations related by <U_vec> <V_vec> <W_vec>.
For the next pass set <nmol> as 3, FIX both these molecules, and search for the next pair.
See examples [1f], [1g], [1h] and example 4. Default = 1.

RESOLUTION <rmin> <rmax>

Can be put in as 4sin(theta)**2/lambda**2 or as Angstrom limits in
any order.

PKLIM <rp>

Output all peaks above <rp*>{maximum peak height}. Default 0.5.

NPIC <np>

Number of peaks to output from the translation function map for each
orientation. Default 10. Be aware that the highest peaks in the translation
function map do not necessarily correspond to the highest correlation coefficients.
All targets are prone to generate "noise" peaks, and good solutions usually
satisfy all 3 criteria: High T1 peak, high correlation coefficient, low Rfactor.

Example

TRAFUN CO NMOL 1 RESO 8 4 PKLIM 0.5 NPIC 10 NCStran 0.03 0.0 0.5

Other optional keywords

SYMMETRY <spg>

(Optional)

Spacegroup name or spacegroup number. It will default to
that of the CRYSTAL data, picked up at the SORTFUN step. You may need to
change it to test other possibilities; e.g. enantiomorphic spacegroups -
P65 instead of P61. If you are not sure of your spacegroup, the translation function
is a good way to distinguish the true spacegroup; e.g. you may need to test all
possible orthorhombic possibilities;
P222; P2 2 21; P2 21 2; P2 21 21; P21 2 2; P 21 2 21; P21 21 2; P 21 21 21;
See example [1d], [1e].

Information used to modify the CRYSTAL amplitudes. See descriptions
above for CLMN.

Example:

CRYSTAL ORTH 1 FLIMI 0.E0 1.E8 SHARP 0.0

Other compulsory keywords

SOLUTION [FIX] <i> <alphai>
<betai> <gammai> [ <Xi> <Yi> <Zi> ]

FIX <i> <alphai> <betai> <gammai> <Xi> <Yi> <Zi>

If the molecule generated by this solution is FIXed, the last 6 parameters
define its position in the cell. Structure factors calculated from this
molecule will be added to those generated for molecules which are being
searched for.

When searching for a single molecule, a list of possible orientations from the rotation
function (labelled SOLUTIONRC in ROTFUN output) is required.

Molecules are found sequentially. When searching for the nth molecule of a
set, there must be sets of (n-1) previously determined solutions to the translation function.
These are labelled with the key word FIX. For example to find the 2nd molecule fix one solution:

SOLUTIONTF1 FIX 1 <alpha1> <beta1> <gamma1> <X1> <Y1> <Z1>

followed by the set of possible rotation function solutions.
Each rotation orientation is tested in turn with the previous input FIXed solution.
If you want to test several translation solutions, you can repeat the
FIX information, and again follow it with the set of possible rotation function
solutions.

There is a limit of 99 (calculated as NMOL* Number_of_solutionrc)
on the number of orientation solutions which can be included in one run.
However there is no extra overhead
in submitting several runs. This list should come last and is terminated
by end-of-file or the keyword END.

The list of solutions can be extracted from ROTFUN (and TRAFUN) output using grep
and edited in here.

<i>

<i> is the number for the appropriate table<i>.

<alphai> <betai> <gammai>

Euler angles output by ROTFUN. If there are no clear maxima you should
test many solutions. Correct solutions have been found from rotation solutions
which were far down the list.

HINTS

To extract the rotation information, `grep' (Unix)
for `SOLUTIONRC' in the ROTFUN output. Edit the resulting list to include
only those solutions you want to run the translation search on, and include
them in the input data e.g. with `@<file>'.

If you are searching for the <nmol>th molecule of a set, you must
FIX <nmol>-1 solutions and search for the <nmol>th one. You
will probably have several sets of the fixed solutions to test, plus many
possible orientation solutions.

FIXed solutions will be extracted from your previous TRAFUN log. They
will be followed by the list of solutions to the Rotation function output
by Step_3. Structure factors calculated from the FIXed solutions are added
to those generated for search molecules.

To extract the information for FIXed, grep for `SOLUTIONTF'.
You will need to sort these to find those with the highest correlation
coefficients, and lowest Rfactors.

FITFUN keywords {Step_5}

This signals the beginning of Step_5 FITFUN which performs Rigid-body
refinement. It minimises the sum over all hkl of ({Fo*exp(-Bs**2)}**2 -
{k*Fc**2})**2 with respect to scale, B-factor and rotation and translation
parameters.

Subsidiary words after FITFUN (many same as TRAFUN):

NMOL <nmol>

Number of molecules to fit. All are fitted together by an iterative
procedure.

RESOLUTION <rmin> <rmax>

Can be put in as 4sin(theta)**2/lambda**2 or as Angstrom limits in
any order. Often sensible to "fit" the molecules against high resolution data if the
sequence homology is close.

ITER <niter>

Number of iterations (default 10).

CONV <con>

Convergence acceptance (default 0.001).

Example

FITFUN NMOL 3 RESO 20 4.5 ITER 10 CONV 1.E-3

Extra keywords

Information used to modify the CRYSTAL amplitudes. See descriptions
above for CLMN.

SYMM <spg>

(Optional)

Spacegroup name or spacegroup number. It will default to
that of the CRYSTAL data, picked up at the SORTFUN step. You may need to
change it to test other possibilities; e.g. enantiomorphic spacegroups -
P65 instead of P61.

REFSOLUTION [ BF ] [ AL ] [ BE ] [ GA ] [ X ] [ Y ] [ Z ]

Refinement to be done for any of temperature factor, alpha, beta, gamma,
x, y, z. Remember - in polar spacegroups you cannot refine either y or
z parameter for one solution.
This defaults to sensible values for different space groups.

Optional: program chooses sensible defaults.

Example

REFSOL AL BE GA X Y Z BF

SOLUTION <i> <alphai> <betai>
<gammai> [ <Xi> <Yi> <Zi> ]

<i>

Model number for input. Different solutions may require different
model numbers. Assign all table<i>.

<alphai> <betai> <gammai>

Euler angles output by ROTFUN. If there is no clear maximum you should
test many solutions. Correct solutions have been found from rotation solutions
which were far down the list.

<Xi> <Yi> <Zi> [ <CCi> <RFi> ]

These three parameters define the molecules position in the cell.
It is often convenient to keep the correlation coefficient and R factor
on the solution line. It helps to monitor solutions - subsequent steps
should improve these parameters! The solutions are refined in sets of
NMOL. There may be up to 99 solutions given (99/NMOL sets).

This list of Eulerian angles and translations can be extracted from
the log file and edited in here. To extract the information from the previous
log file, grep for `SOLUTIONTF'. You will need to sort these to find those
with the highest correlation coefficients, and lowest Rfactors as described
in step_4a, and edit to include only those solutions you want to run the
rigid body refinement on to include them in the input data.

Reorientate stage. Moves Eulerian angle solutions determined for shifted
model stored in XYZOUT<i> to give solutions to be applied to original
MODEL. Needed if you want your solutions converted back to ones to apply
to original coordinates.

COM <Xcom> <Ycom> <Zcom>

coordinates of the molecules centre of mass output by TABFUN

EULER <alpha> <beta> <gamma>

rotation angles applied to the original model output by TABFUN.

Example

SHIFT 1 COM 17.3 -10.5 28.7 EULER 301.2 35.7 185.2

REORIENTATE keywords {Step_6}

This signals the beginning of Step_6 - reorientate stage. This step
can be run as a standalone step or as part of ROTFUN or FITFUN.
It moves Eulerian angle solutions determined for shifted model stored in
XYZOUT<i> to give solutions to be applied to original MODEL. Needed
if you want your solutions converted back to ones to apply to original
coordinates.

COM <Xcom> <Ycom> <Zcom>

Coordinates of the molecule's centre of mass output by TABFUN

EULER <alpha> <beta>
<gamma>

Rotation angles applied to the original model output by TABFUN.

Example

SHIFT 1 COM 17.3 -10.5 28.7 EULER 301.2 35.7 185.2

Compulsory following keyword

SOLUTION <i> <alphai>
<betai> <gammai> <Xi> <Yi> <Zi>

There may be up to 99 solutions given. This list is terminated by end-of-file
or the keyword END.

END

Must be last keyword. Used as termination for list of solutions.

NOTES

Memory allocation

The program has been made more memory-efficient, but still uses a lot, at several points
a whole Fourier transform is held in memory. The defaults are estimated to allow the
observed and tabulated structure factors to be stored. However if the estimate is too
low it is able to use dynamic memory allocation; the amount to be allocated at runtime
is parameterised by assigning values to logical names. There
may be some trial and error involved in setting appropriate values.

If the allocation for an array isn't large enough, the program stops
with a message which should indicate at least which parameter needs to
be increased and, in most cases, to what value. If the message doesn't
make it clear what needs to be increased, please report the fact. Using
the keyword VERBOSE may give more indication. The current values are printed
in the output (look for `Memory allocation'). They may be changed by giving
the appropriate logical names an integer value (which represents the size
of an array) in any of possible ways:

The last option may be most appropriate on a system with lots of memory
to provide large defaults and the distributed default.def contains commented-out
values for a `big' version used at York and Cambridge.

Rotation matrix definitions

The convention is that the orthogonalised coordinates of "crystal 2" (usually the model)
are rotated to overlap the orthogonalised coordinates of crystal 1.

i.e. [XO1] = [ROT] [XO2]
[YO1] [YO2]
[ZO1] [ZO2]

This means that axis permutations introduced by using NCODE = 2, 3 or 4
will result in apparently different solutions, although the effect on the
fractional coordinates is the same.

In Polar angles:

If l m n are the direction cosines of the axis about which the
rotation k = kappa takes place, and: